null Sun 23 Dec 22:23:05 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vpm-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vpm-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vpm-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vpm-3.6-parrot-hancs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vpm-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vpm-3.6-parrot-hancs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Sun 23 Dec 22:23:13 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vpm-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vpm-3.6-parrot-hancs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 338 and 0 Target number of residues in the AU: 338 Target solvent content: 0.6553 Checking the provided sequence file Detected sequence length: 169 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 3 Adjusted target number of residues: 507 Adjusted target solvent content: 0.48 Input MTZ file: 1vpm-3.6-parrot-hancs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 24 Cell parameters: 82.941 106.484 120.177 90.000 90.000 90.000 Input sequence file: 1vpm-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 4056 target number of atoms Had to go as low as 0.55 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 3 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 79.699 3.600 Wilson plot Bfac: 81.12 6312 reflections ( 97.92 % complete ) and 0 restraints for refining 4511 atoms. Observations/parameters ratio is 0.35 ------------------------------------------------------ Starting model: R = 0.3159 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2894 (Rfree = 0.000) for 4511 atoms. Found 28 (28 requested) and removed 77 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.51 3.60 Search for helices and strands: 0 residues in 0 chains, 4553 seeds are put forward NCS extension: 0 residues added, 4553 seeds are put forward Round 1: 234 peptides, 43 chains. Longest chain 11 peptides. Score 0.375 Round 2: 275 peptides, 39 chains. Longest chain 17 peptides. Score 0.537 Round 3: 301 peptides, 40 chains. Longest chain 18 peptides. Score 0.589 Round 4: 317 peptides, 31 chains. Longest chain 40 peptides. Score 0.704 Round 5: 316 peptides, 38 chains. Longest chain 21 peptides. Score 0.640 Taking the results from Round 4 Chains 34, Residues 286, Estimated correctness of the model 50.8 % 6 chains (84 residues) have been docked in sequence Building loops using Loopy2018 34 chains (286 residues) following loop building 6 chains (84 residues) in sequence following loop building ------------------------------------------------------ 6312 reflections ( 97.92 % complete ) and 7244 restraints for refining 3676 atoms. 5864 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2401 (Rfree = 0.000) for 3676 atoms. Found 23 (23 requested) and removed 97 (11 requested) atoms. Cycle 2: After refmac, R = 0.2226 (Rfree = 0.000) for 3535 atoms. Found 11 (23 requested) and removed 52 (11 requested) atoms. Cycle 3: After refmac, R = 0.2113 (Rfree = 0.000) for 3471 atoms. Found 6 (21 requested) and removed 24 (11 requested) atoms. Cycle 4: After refmac, R = 0.2030 (Rfree = 0.000) for 3439 atoms. Found 7 (21 requested) and removed 28 (11 requested) atoms. Cycle 5: After refmac, R = 0.1984 (Rfree = 0.000) for 3407 atoms. Found 1 (19 requested) and removed 22 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.53 3.63 Search for helices and strands: 0 residues in 0 chains, 3497 seeds are put forward NCS extension: 58 residues added (23 deleted due to clashes), 3555 seeds are put forward Round 1: 258 peptides, 44 chains. Longest chain 12 peptides. Score 0.433 Round 2: 283 peptides, 37 chains. Longest chain 20 peptides. Score 0.578 Round 3: 298 peptides, 38 chains. Longest chain 20 peptides. Score 0.602 Round 4: 299 peptides, 38 chains. Longest chain 32 peptides. Score 0.604 Round 5: 299 peptides, 38 chains. Longest chain 19 peptides. Score 0.604 Taking the results from Round 5 Chains 38, Residues 261, Estimated correctness of the model 16.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6312 reflections ( 97.92 % complete ) and 7908 restraints for refining 3523 atoms. 6902 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2075 (Rfree = 0.000) for 3523 atoms. Found 15 (20 requested) and removed 112 (11 requested) atoms. Cycle 7: After refmac, R = 0.1930 (Rfree = 0.000) for 3416 atoms. Found 4 (19 requested) and removed 47 (10 requested) atoms. Cycle 8: After refmac, R = 0.1866 (Rfree = 0.000) for 3372 atoms. Found 9 (19 requested) and removed 16 (10 requested) atoms. Cycle 9: After refmac, R = 0.1841 (Rfree = 0.000) for 3358 atoms. Found 8 (19 requested) and removed 15 (10 requested) atoms. Cycle 10: After refmac, R = 0.1794 (Rfree = 0.000) for 3350 atoms. Found 0 (19 requested) and removed 16 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.54 3.64 Search for helices and strands: 0 residues in 0 chains, 3473 seeds are put forward NCS extension: 32 residues added (1 deleted due to clashes), 3505 seeds are put forward Round 1: 251 peptides, 42 chains. Longest chain 11 peptides. Score 0.438 Round 2: 271 peptides, 34 chains. Longest chain 21 peptides. Score 0.582 Round 3: 277 peptides, 34 chains. Longest chain 24 peptides. Score 0.596 Round 4: 283 peptides, 34 chains. Longest chain 21 peptides. Score 0.609 Round 5: 266 peptides, 30 chains. Longest chain 22 peptides. Score 0.612 Taking the results from Round 5 Chains 33, Residues 236, Estimated correctness of the model 19.3 % 4 chains (32 residues) have been docked in sequence ------------------------------------------------------ 6312 reflections ( 97.92 % complete ) and 7635 restraints for refining 3488 atoms. 6635 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2150 (Rfree = 0.000) for 3488 atoms. Found 20 (20 requested) and removed 73 (11 requested) atoms. Cycle 12: After refmac, R = 0.1967 (Rfree = 0.000) for 3421 atoms. Found 6 (20 requested) and removed 29 (11 requested) atoms. Cycle 13: After refmac, R = 0.1916 (Rfree = 0.000) for 3389 atoms. Found 7 (19 requested) and removed 19 (10 requested) atoms. Cycle 14: After refmac, R = 0.1866 (Rfree = 0.000) for 3376 atoms. Found 1 (19 requested) and removed 21 (10 requested) atoms. Cycle 15: After refmac, R = 0.1849 (Rfree = 0.000) for 3352 atoms. Found 4 (19 requested) and removed 16 (10 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.53 3.63 Search for helices and strands: 0 residues in 0 chains, 3442 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 3460 seeds are put forward Round 1: 237 peptides, 37 chains. Longest chain 20 peptides. Score 0.460 Round 2: 255 peptides, 34 chains. Longest chain 21 peptides. Score 0.543 Round 3: 264 peptides, 36 chains. Longest chain 22 peptides. Score 0.543 Round 4: 258 peptides, 34 chains. Longest chain 29 peptides. Score 0.550 Round 5: 257 peptides, 34 chains. Longest chain 21 peptides. Score 0.548 Taking the results from Round 4 Chains 36, Residues 224, Estimated correctness of the model 0.0 % 2 chains (44 residues) have been docked in sequence ------------------------------------------------------ 6312 reflections ( 97.92 % complete ) and 7630 restraints for refining 3557 atoms. 6608 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2199 (Rfree = 0.000) for 3557 atoms. Found 20 (20 requested) and removed 48 (11 requested) atoms. Cycle 17: After refmac, R = 0.2012 (Rfree = 0.000) for 3524 atoms. Found 4 (20 requested) and removed 29 (11 requested) atoms. Cycle 18: After refmac, R = 0.1958 (Rfree = 0.000) for 3494 atoms. Found 8 (20 requested) and removed 18 (11 requested) atoms. Cycle 19: After refmac, R = 0.1893 (Rfree = 0.000) for 3483 atoms. Found 3 (20 requested) and removed 16 (11 requested) atoms. Cycle 20: After refmac, R = 0.1865 (Rfree = 0.000) for 3465 atoms. Found 8 (20 requested) and removed 19 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.52 3.62 Search for helices and strands: 0 residues in 0 chains, 3557 seeds are put forward NCS extension: 30 residues added (1 deleted due to clashes), 3587 seeds are put forward Round 1: 219 peptides, 40 chains. Longest chain 15 peptides. Score 0.368 Round 2: 247 peptides, 36 chains. Longest chain 20 peptides. Score 0.499 Round 3: 272 peptides, 35 chains. Longest chain 26 peptides. Score 0.573 Round 4: 259 peptides, 31 chains. Longest chain 22 peptides. Score 0.585 Round 5: 273 peptides, 35 chains. Longest chain 32 peptides. Score 0.576 Taking the results from Round 4 Chains 32, Residues 228, Estimated correctness of the model 8.7 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 6312 reflections ( 97.92 % complete ) and 8135 restraints for refining 3595 atoms. 7186 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2055 (Rfree = 0.000) for 3595 atoms. Found 16 (21 requested) and removed 33 (11 requested) atoms. Cycle 22: After refmac, R = 0.1951 (Rfree = 0.000) for 3564 atoms. Found 6 (20 requested) and removed 21 (11 requested) atoms. Cycle 23: After refmac, R = 0.1887 (Rfree = 0.000) for 3547 atoms. Found 4 (20 requested) and removed 12 (11 requested) atoms. Cycle 24: After refmac, R = 0.1982 (Rfree = 0.000) for 3535 atoms. Found 9 (20 requested) and removed 18 (11 requested) atoms. Cycle 25: After refmac, R = 0.1944 (Rfree = 0.000) for 3520 atoms. Found 4 (20 requested) and removed 18 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.52 3.62 Search for helices and strands: 0 residues in 0 chains, 3618 seeds are put forward NCS extension: 44 residues added (3 deleted due to clashes), 3662 seeds are put forward Round 1: 227 peptides, 39 chains. Longest chain 18 peptides. Score 0.405 Round 2: 254 peptides, 38 chains. Longest chain 14 peptides. Score 0.494 Round 3: 261 peptides, 37 chains. Longest chain 18 peptides. Score 0.524 Round 4: 274 peptides, 39 chains. Longest chain 18 peptides. Score 0.535 Round 5: 283 peptides, 38 chains. Longest chain 21 peptides. Score 0.568 Taking the results from Round 5 Chains 40, Residues 245, Estimated correctness of the model 1.7 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 6312 reflections ( 97.92 % complete ) and 7883 restraints for refining 3594 atoms. 6904 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2002 (Rfree = 0.000) for 3594 atoms. Found 21 (21 requested) and removed 26 (11 requested) atoms. Cycle 27: After refmac, R = 0.1820 (Rfree = 0.000) for 3582 atoms. Found 7 (21 requested) and removed 16 (11 requested) atoms. Cycle 28: After refmac, R = 0.1775 (Rfree = 0.000) for 3568 atoms. Found 10 (20 requested) and removed 14 (11 requested) atoms. Cycle 29: After refmac, R = 0.1723 (Rfree = 0.000) for 3559 atoms. Found 8 (20 requested) and removed 36 (11 requested) atoms. Cycle 30: After refmac, R = 0.1683 (Rfree = 0.000) for 3529 atoms. Found 4 (20 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.53 3.63 Search for helices and strands: 0 residues in 0 chains, 3646 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 3663 seeds are put forward Round 1: 221 peptides, 41 chains. Longest chain 13 peptides. Score 0.361 Round 2: 262 peptides, 34 chains. Longest chain 17 peptides. Score 0.560 Round 3: 238 peptides, 35 chains. Longest chain 19 peptides. Score 0.487 Round 4: 242 peptides, 35 chains. Longest chain 18 peptides. Score 0.498 Round 5: 254 peptides, 36 chains. Longest chain 16 peptides. Score 0.518 Taking the results from Round 2 Chains 34, Residues 228, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6312 reflections ( 97.92 % complete ) and 7927 restraints for refining 3583 atoms. 7049 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1810 (Rfree = 0.000) for 3583 atoms. Found 14 (20 requested) and removed 17 (11 requested) atoms. Cycle 32: After refmac, R = 0.1675 (Rfree = 0.000) for 3571 atoms. Found 5 (20 requested) and removed 12 (11 requested) atoms. Cycle 33: After refmac, R = 0.1627 (Rfree = 0.000) for 3561 atoms. Found 3 (20 requested) and removed 11 (11 requested) atoms. Cycle 34: After refmac, R = 0.1600 (Rfree = 0.000) for 3551 atoms. Found 3 (20 requested) and removed 11 (11 requested) atoms. Cycle 35: After refmac, R = 0.1587 (Rfree = 0.000) for 3540 atoms. Found 2 (20 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.56 3.66 Search for helices and strands: 0 residues in 0 chains, 3622 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 3642 seeds are put forward Round 1: 221 peptides, 39 chains. Longest chain 12 peptides. Score 0.387 Round 2: 230 peptides, 32 chains. Longest chain 20 peptides. Score 0.501 Round 3: 212 peptides, 30 chains. Longest chain 17 peptides. Score 0.476 Round 4: 200 peptides, 29 chains. Longest chain 20 peptides. Score 0.455 Round 5: 220 peptides, 31 chains. Longest chain 18 peptides. Score 0.486 Taking the results from Round 2 Chains 32, Residues 198, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6312 reflections ( 97.92 % complete ) and 8325 restraints for refining 3631 atoms. 7565 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1781 (Rfree = 0.000) for 3631 atoms. Found 11 (21 requested) and removed 14 (11 requested) atoms. Cycle 37: After refmac, R = 0.1731 (Rfree = 0.000) for 3617 atoms. Found 8 (21 requested) and removed 11 (11 requested) atoms. Cycle 38: After refmac, R = 0.1888 (Rfree = 0.000) for 3608 atoms. Found 13 (21 requested) and removed 24 (11 requested) atoms. Cycle 39: After refmac, R = 0.1594 (Rfree = 0.000) for 3590 atoms. Found 11 (21 requested) and removed 14 (11 requested) atoms. Cycle 40: After refmac, R = 0.1520 (Rfree = 0.000) for 3584 atoms. Found 12 (21 requested) and removed 18 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.51 3.60 Search for helices and strands: 0 residues in 0 chains, 3672 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 3690 seeds are put forward Round 1: 163 peptides, 30 chains. Longest chain 9 peptides. Score 0.326 Round 2: 213 peptides, 31 chains. Longest chain 15 peptides. Score 0.467 Round 3: 208 peptides, 33 chains. Longest chain 16 peptides. Score 0.426 Round 4: 226 peptides, 29 chains. Longest chain 25 peptides. Score 0.527 Round 5: 226 peptides, 31 chains. Longest chain 17 peptides. Score 0.503 Taking the results from Round 4 Chains 31, Residues 197, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 6312 reflections ( 97.92 % complete ) and 8412 restraints for refining 3675 atoms. 7625 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1674 (Rfree = 0.000) for 3675 atoms. Found 14 (21 requested) and removed 22 (11 requested) atoms. Cycle 42: After refmac, R = 0.1529 (Rfree = 0.000) for 3660 atoms. Found 8 (21 requested) and removed 14 (11 requested) atoms. Cycle 43: After refmac, R = 0.1481 (Rfree = 0.000) for 3652 atoms. Found 3 (21 requested) and removed 11 (11 requested) atoms. Cycle 44: After refmac, R = 0.1460 (Rfree = 0.000) for 3642 atoms. Found 5 (21 requested) and removed 11 (11 requested) atoms. Cycle 45: After refmac, R = 0.1426 (Rfree = 0.000) for 3635 atoms. Found 3 (21 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.53 3.63 Search for helices and strands: 0 residues in 0 chains, 3740 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 3755 seeds are put forward Round 1: 153 peptides, 29 chains. Longest chain 16 peptides. Score 0.306 Round 2: 182 peptides, 29 chains. Longest chain 15 peptides. Score 0.401 Round 3: 185 peptides, 27 chains. Longest chain 17 peptides. Score 0.437 Round 4: 191 peptides, 29 chains. Longest chain 16 peptides. Score 0.428 Round 5: 202 peptides, 29 chains. Longest chain 21 peptides. Score 0.461 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 29, Residues 173, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 1vpm-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6312 reflections ( 97.92 % complete ) and 8808 restraints for refining 3677 atoms. 8145 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1651 (Rfree = 0.000) for 3677 atoms. Found 0 (21 requested) and removed 11 (11 requested) atoms. Cycle 47: After refmac, R = 0.1574 (Rfree = 0.000) for 3655 atoms. Found 0 (21 requested) and removed 7 (11 requested) atoms. Cycle 48: After refmac, R = 0.1601 (Rfree = 0.000) for 3643 atoms. Found 0 (21 requested) and removed 9 (11 requested) atoms. Cycle 49: After refmac, R = 0.1594 (Rfree = 0.000) for 3631 atoms. Found 0 (21 requested) and removed 8 (11 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:21:20 GMT 2018 Job finished. TimeTaking 58.26 Used memory is bytes: 2378448